MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Gene	description	Rank	Filtered	green	Value Type	Interaction Map	Network Comparison Type	red	network_comparison

Results: HTML CSV LaTeX

Showing element 451 to 500 of 38536 in total

Network Comparison Type  : Divided

description	Rank	Filtered	green	Value Type	Interaction Map	red	network_comparison
3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193]	2627	1	75.4487	Rooted	Low confidence	73.0199	1.03326
	3147		0.00001	Measured	High confidence	0.00001	1
				Ranked
				Squared
				Rooted
	3493		8292.57	Measured	Low confidence	8082.12	1.02604
3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	299	0	11512.3	Ranked	High confidence	12338.7	1.07178
	438		44.9836	Rooted		43.8864	1.025
	453		11512.3	Ranked	Low confidence	12338.7	1.07178
	492		5046.33	Measured	High confidence	5038.33	1.00159
	493		17901.1	Squared		17901.1	1
	662		44.9836	Rooted	Low confidence	43.8864	1.025
	822		5046.33	Measured		5038.33	1.00159
	836		17901.1	Squared		17901.1	1
	1073	1	42724.1			44737.4	1.04712
	1663		193.866	Ranked		197.872	1.02066
	2622		75.4487	Rooted		73.0199	1.03326
	2756		0.00001	Measured	High confidence	0.00001	1
				Ranked
				Squared
				Rooted
	3487		8292.57	Measured	Low confidence	8082.12	1.02604
3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type i (3beta-hsd i) (trophoblast antigen fdo161g) [includes: 3-beta-hydroxy- delta(5)-steroid dehydrogenase (ec 1.1.1.145) (3-beta-hydroxy-5-ene steroid dehydrogenase) (progesterone reductase); steroid delta- isomerase (ec 5.3.3.1) (delta-5-3-ketosteroid isomerase)]. [swissprot;acc:p14060]	1075		42724.1	Squared		44737.4	1.04712
	1665		193.866	Ranked		197.872	1.02066
	2624		75.4487	Rooted		73.0199	1.03326
	2802		0.00001	Measured	High confidence	0.00001	1
				Ranked
				Squared
				Rooted
	3489		8292.57	Measured	Low confidence	8082.12	1.02604
3'(2'), 5'-bisphosphate nucleotidase 1; bisphosphate 3'-nucleotidase; bpntase; pap-inositol-1,4-phosphatase. [refseq;acc:nm_006085]	178		221.607	Ranked		209.954	1.0555
	2650		36053.6	Squared		37407.8	1.03756
	4603		65.5857	Rooted		66.9425	1.02069
	4994		6911.72	Measured		6922.79	1.0016
3'-5' rna exonuclease; polynucleotide phosphorylase-like. [refseq;acc:nm_033109]	1373		201.696	Ranked		206.13	1.02198
	1388		72.4192	Rooted		69.8381	1.03696
	2310		7838.4	Measured		7602.32	1.03105
	2740		41084.3	Squared		42607.1	1.03707
3-hydroxy-3-methylglutaryl-coenzyme a reductase (ec 1.1.1.34) (hmg-coa reductase). [swissprot;acc:p04035]	1118		31123.3		High confidence	27234.2	1.1428
	2302		7263.68	Measured		6946.6	1.04565
	2303		192.542	Ranked		191.567	1.00509
	2488		72.2598	Rooted		71.4412	1.01146
	3121		43211.7	Squared	Low confidence	44716.9	1.03483
	3261		196.642	Ranked		199.744	1.01577
	3321		8238.4	Measured		8023.42	1.02679
	3423		74.7129	Rooted		72.5008	1.03051
3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [swissprot;acc:q99714]	1886		43022.5	Squared		44788.1	1.04104
	3180		0.00001	Measured	High confidence	0.00001	1
				Ranked
				Squared

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.